MRG: clean up index to use MultiCollection
#451
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ctb
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MultiCollectionMultiCollection
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Sep 9, 2024
…450) * use recursion to load paths into a MultiCollection => mf support * MRG: clean up index to use `MultiCollection` (#451) * try making index work with standard code * kinda working * fmt * refactor * clear up the tests * refactor/clean up * cargo fmt * add tests for index warning & error * comment
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Oct 15, 2024
…r database (#430) * refactor & rename & consolidate * remove 'lower' * add cargo doc output for private fn * add a few comments/docs * switch to dev version of sourmash * tracking * cleaner * cleanup * load rocksdb natively * foo * cargo fmt * upd * upd * fix fmt * MRG: create `MultiCollection` for collections that span multiple files (#434) * preliminary victory * compiles and mostly runs * cleanup, split to new module * cleanup and comment * more cleanup of diff * cargo fmt * fix fmt * restore n_failed * comment failing test * cleanup and de-vec * create module/submodule structure * comment for later * get rid of vec * beg for help * cleanup and doc * clippy fixes * compiling again * cleanup * bump sourmash to v0.15.1 * check if is rocksdb * weird error * use remove_unwrap branch of sourmash * get index to work with MultiCollection * old bug now fixed * clippy, format, and fix * make names clearer * ditch MultiCollection for index, at least for now * testy testy * getting closer * update sourmash * mark failing tests * upd * cargo fmt * MRG: test exit from `pairwise` and `multisearch` if no loaded sketches (#437) * upd * check for appropriate multisearch error exits * add more tests for pairwise, too * cargo fmt * MRG: switch to more efficient use of `Collection` by removing cloning (#438) * remove unnecessary clones by switch to references in SmallSignature * switch away from references for collections => avoid clones * remove MultiCollection::iter * MRG: add tests for RocksDB/RevIndex, standalone manifests, and flexible pathlists (#436) * test using rocksdb as source of sketches * test file lists of zips * cargo fmt * hackity hack hack a picklist * ok that makes more sense * it works * comments around future par_iter * support loading from a .sig.gz for index * test pairwise loading from rocksdb * add test for queries from Rocksdb * decide not to implement lists of manifests :) * reenable and fix test_fastgather.py::test_indexed_against * impl Deref for MultiCollection * clippy * switch to using load_sketches method * deref doesn't actually make sense for MultiCollection * update to latest sourmash code * update to latest sourmash code * simplify * update to latest sourmash code * remove unnecessary flag * MRG: support & test loading of standalone manifests within pathlists (#450) * use recursion to load paths into a MultiCollection => mf support * MRG: clean up index to use `MultiCollection` (#451) * try making index work with standard code * kinda working * fmt * refactor * clear up the tests * refactor/clean up * cargo fmt * add tests for index warning & error * comment * MRG: documentation updates based on new collection loading (#444) * update docs for #430 * upd documentation * upd * Update src/lib.rs Co-authored-by: Tessa Pierce Ward <[email protected]> * switch unwrap to expect * move unwrap to expect * minor cleanup * cargo fmt * provide legacy method to avoid xfail on index loading * switch to using reference * update docs to reflect pathlist behavior * test recursive nature of MultiCollection * re-enable test that is now passing * update to latest sourmash * upd sourmash * update sourmash * mut MultiCollection * cleanup * update after merge of sourmash-bio/sourmash#3305 * fix contains_revindex * add trace commands for tracing loading * use released version of sourmash * add support for ignoring abundance * cargo fmt * avoid downsampling until we know there is overlap * change downsample to true; add panic assertion * move downsampling side guard * eliminate redundant overlap check * move calc_abund_stats * extract abundance code into own function; avoid downsampling if poss * cleanup * fmt * update to next sourmash release * cargo fmt * upd sourmash * correct numbers * upd sourmash * upd sourmash * upd sourmash * upd sourmash * use new try_into() and eliminate several clone()s * refactor a bit more * deallocate collection? * upd sourmash * cargo fmt * fix merge foo --------- Co-authored-by: Tessa Pierce Ward <[email protected]>
ctb
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Oct 15, 2024
…#471) * refactor & rename & consolidate * remove 'lower' * add cargo doc output for private fn * add a few comments/docs * switch to dev version of sourmash * tracking * cleaner * cleanup * load rocksdb natively * foo * cargo fmt * upd * upd * fix fmt * MRG: create `MultiCollection` for collections that span multiple files (#434) * preliminary victory * compiles and mostly runs * cleanup, split to new module * cleanup and comment * more cleanup of diff * cargo fmt * fix fmt * restore n_failed * comment failing test * cleanup and de-vec * create module/submodule structure * comment for later * get rid of vec * beg for help * cleanup and doc * clippy fixes * compiling again * cleanup * bump sourmash to v0.15.1 * check if is rocksdb * weird error * use remove_unwrap branch of sourmash * get index to work with MultiCollection * old bug now fixed * clippy, format, and fix * make names clearer * ditch MultiCollection for index, at least for now * testy testy * getting closer * update sourmash * mark failing tests * upd * cargo fmt * MRG: test exit from `pairwise` and `multisearch` if no loaded sketches (#437) * upd * check for appropriate multisearch error exits * add more tests for pairwise, too * cargo fmt * MRG: switch to more efficient use of `Collection` by removing cloning (#438) * remove unnecessary clones by switch to references in SmallSignature * switch away from references for collections => avoid clones * remove MultiCollection::iter * MRG: add tests for RocksDB/RevIndex, standalone manifests, and flexible pathlists (#436) * test using rocksdb as source of sketches * test file lists of zips * cargo fmt * hackity hack hack a picklist * ok that makes more sense * it works * comments around future par_iter * support loading from a .sig.gz for index * test pairwise loading from rocksdb * add test for queries from Rocksdb * decide not to implement lists of manifests :) * reenable and fix test_fastgather.py::test_indexed_against * impl Deref for MultiCollection * clippy * switch to using load_sketches method * deref doesn't actually make sense for MultiCollection * update to latest sourmash code * update to latest sourmash code * simplify * update to latest sourmash code * remove unnecessary flag * MRG: support & test loading of standalone manifests within pathlists (#450) * use recursion to load paths into a MultiCollection => mf support * MRG: clean up index to use `MultiCollection` (#451) * try making index work with standard code * kinda working * fmt * refactor * clear up the tests * refactor/clean up * cargo fmt * add tests for index warning & error * comment * MRG: documentation updates based on new collection loading (#444) * update docs for #430 * upd documentation * upd * Update src/lib.rs Co-authored-by: Tessa Pierce Ward <[email protected]> * switch unwrap to expect * move unwrap to expect * minor cleanup * cargo fmt * provide legacy method to avoid xfail on index loading * switch to using reference * update docs to reflect pathlist behavior * test recursive nature of MultiCollection * re-enable test that is now passing * update to latest sourmash * upd sourmash * update sourmash * mut MultiCollection * cleanup * update after merge of sourmash-bio/sourmash#3305 * fix contains_revindex * add trace commands for tracing loading * use released version of sourmash * add support for ignoring abundance * cargo fmt * avoid downsampling until we know there is overlap * change downsample to true; add panic assertion * move downsampling side guard * eliminate redundant overlap check * move calc_abund_stats * extract abundance code into own function; avoid downsampling if poss * cleanup * fmt * update to next sourmash release * cargo fmt * upd sourmash * correct numbers * upd sourmash * upd sourmash * upd sourmash * upd sourmash * use new try_into() and eliminate several clone()s * refactor a bit more * use new try_into() in manysearch; flag clones * avoid a few more clones * eliminate more clone * fix mismatched clauses * note minhash * fix mastiff_manygather * avoid more clone * resolve comments * microchange * microchange 2 * eliminate more clone: fastgather * avoid more clone: fastmultigather * refactor to avoid more clones * rm one more clone * cleanup * cargo fmt * cargo fmt * deallocate collection? * deallocate collection? * upd sourmash * cargo fmt * fix merge foo * try out new sourmash PR * upd latest sourmash branch * upd sourmash --------- Co-authored-by: Tessa Pierce Ward <[email protected]>
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NOTE: PR into #450
This PR adjust
MultiCollectionto load sketches into memory if internal storage is specified, which allowsindexto index anything loadable byMultiCollectionas long as it fits into memory.ref @olgabot request here
TODO: